Endogenous oxidative stress is believed to play a key role in the pathogenesis of mitochondrial diseases (MD). In this group of heterogeneous disorders the increased production of radical species caused by compromised mitochondrial respiratory function could affect both mitochondrial and nuclear DNA integrity. The aim of the present study was to assess the basal level of nuclear DNA (nDNA) damage in terms of chromosome and DNA alterations in leukocytes of 13 patients (age range 29-74 years) presenting several forms of MD. A further objective of this work was the evaluation of possible changes in nDNA in a subgroup of patients (10 individuals) before and after a 2 week therapy with ubidecarenone, a coenzyme Q10 analogue. The extent of cytogenetic damage, expressed as chromosome breakage and chromosome loss, was assessed employing the cytokinesis block micronucleus method in cultured peripheral blood lymphocytes, coupled with fluorescence in situ hybridization analysis using a digoxigenin-labelled pancentromeric DNA probe. A modified version of the single cell gel electrophoresis assay was used to quantify primary and oxidative DNA damage in leukocytes. In MD patients an increased level of chromosome damage, expressed as frequency of micronucleated lymphocytes, was detected in comparison with healthy individuals of corresponding sex, age and lifestyle. The FISH analysis revealed a preferential occurrence of micronuclei arising from loss of whole chromosomes in patients, with no substantial difference in frequencies observed in matched controls. The Comet assay indicated a slightly higher level of primary DNA damage in patients compared with controls and also a difference in oxidative DNA damage, however, this was not statistically significant. Patients receiving ubidecarenone showed a statistically significant reduction in the frequency of micronucleated cells after therapy, while only a slight decrease was observed in the levels of both primary DNA damage and oxidized bases.